Align Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; EC 4.1.3.17; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.1.112; Regulator of ribonuclease activity homolog; RraA-like protein (uncharacterized)
to candidate CA265_RS13680 CA265_RS13680 dimethylmenaquinone methyltransferase
Query= curated2:Q9KBI9 (210 letters) >FitnessBrowser__Pedo557:CA265_RS13680 Length = 234 Score = 79.0 bits (193), Expect = 7e-20 Identities = 67/210 (31%), Positives = 99/210 (47%), Gaps = 29/210 (13%) Query: 17 TTCISDALD--GLTN--LTSTIKPLNENDQVVGPARTVQVASGDNLAVLKAMYEASPGDV 72 T I D +D GL + L I+PL+ + V G A TV A VL+ S + Sbjct: 24 TAVIGDIMDKMGLLHQFLPPQIQPLHPDMFVAGRAMTVLEAD-----VLECGQHESSNPI 78 Query: 73 I------VIDAKGD--------CTR-----AIAGDFVLGMAKTLGIAGFVVDGAIRDIRA 113 + +++A D CT A+ G+ + A+ LG AG VVDG RD R Sbjct: 79 LKKPFGLMLEALDDLKKHEVYICTGSSPNYALWGELMSTRAQMLGAAGAVVDGYSRDTRG 138 Query: 114 SKALNFPIFCRGTTIAASKKTG-IGNINVPISCGGVPIRPGDLIVGDADGVTVIPKGQEE 172 LNFP F G G + + VPI GV + PGDL++GD DGV ++PK E Sbjct: 139 ILHLNFPSFSYGNYAQDQAPRGKVIDFRVPIEIKGVLVNPGDLVIGDIDGVCIVPKQHEV 198 Query: 173 NVLQKAKKKQADDEARERAISDNVMAIRAY 202 V+ +A +K ++ ++ I + + A A+ Sbjct: 199 EVVTRALEKARGEKMVQKKILEGMSAKEAF 228 Lambda K H 0.318 0.136 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 132 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 210 Length of database: 234 Length adjustment: 22 Effective length of query: 188 Effective length of database: 212 Effective search space: 39856 Effective search space used: 39856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory